First load the ID's that have already been mapped. Then load the full list with a where clause like the one below in a new table:
WHERE NOT exists(ID)
Then drop the first table(the ones already mapped). What you have left are all of the ID's that weren't previously mapped. At this point I would just map all of these ("all other") and then do a concatenate load to get the ID"s that were already mapped into your table using WHERE NOT exists(ID) again.
There are probably 10 other ways to do this but without knowing every little detail I think this one should be good enough.